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Archiver > GENEALOGY-DNA > 2008-01 > 1199487779


From: "Tim Janzen" <>
Subject: Re: [DNA] Chances for Finding Clade-separating SNP
Date: Fri, 4 Jan 2008 15:02:59 -0800
In-Reply-To: <PM.15352.1199485704@hmweb24.uk1.bibliotech.net>


Dear Gareth,
You may well be right that SNPs that have been reported more than
once are actually simply SNPs occurring in an "overlap" of more than one
fragment in the unassembled sequence fragments of James Watson's genome. If
so, this would help explain why all of the 20 most reported SNPs fall into
three narrow regions on the Y chromosome and why some SNPs that are located
relatively close to each other on the Y chromosome (such as at 11935703 and
11962048) have been reported with the same frequency. If this is the case,
then all 118 SNPs need to be carefully reviewed with equal attention for
potentially being SNPs that subdivide R1b1c and/or R1b1c9, not just the ones
that have been reported most frequently in Ron Scott's file of Watson's
SNPs.
Are there any other large blocks of R1b1c Y DNA sequences available
in public databases that we can look at besides the HUGO Reference Sequence,
Watson's DNA, and Ventor's DNA? If so, where are they and how can we search
them for these 118 SNPs?
Sincerely,
Tim

-----Original Message-----
From:
[mailto:] On Behalf Of Gareth Henson
Sent: Friday, January 04, 2008 2:28 PM
To:
Subject: Re: [DNA] Chances for Finding Clade-separating SNP

I doubt it since some of them are described as "novel".
My guess is that they are the number of hits for the neighbourhood of the
SNP in the unassembled sequence fragments of James Watson's genome. So for
the higher numbers this may mean the SNP was in an "overlap" of several
fragments and/or there were similar sequences generated from other locations
in Watson's genome.

Gareth


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